Evolution and genetics of adaption Flashcards
Adaption definition
A characteristic that enhances the survival of reproduction of organisms that bear it, relative to alternative states
What does the hardy weinburg equation describe
The genetic allele frequency in a population that is not evolving
What does the Hardy weinburg equation predict
The genotype and allele frequencies in one generation from the allele frequencies in the previous generation
What are the assumptions of the hardy weinburg equation
No selection, no mutation and large population, random mating
What is the hardy weinburg equation
p^2 + 2pq+ q^2 = 1
Whats the usefullness of the hardy weinburg equation
Gives a null model
What 4 evolutionary forces are needed to disrupt the hardy weinburg equation
Random mutations, genetic drift, Migration between species and isolated populations and natural selection
Natural selection definition
Differerntial survival and or reproduction of individuals/ any group of reproductive units
How do you work out the fitness of a species
Probability of survival x average number of offspring for a class of individuals
Whats the maximum fitness
w=1
Whats the selection coefficient
The difference between w and 1
How do we know natural selection exists?
Correlations between trait and environment, responses to experimental change in the enviornment, coreelations between trait and fitness component, signatures in the genome
What are the problems with detecting selection?
Genetic drift can spread traits, ancestral state, selection might not cause any change, selection might not be working at the individual level, linkage
What does natural selection not do?
Always lead to adaptation, produce perfection, always progress, produce a balanced, harmonious world, consider ethics
What is the levels of standing genetic variation
Presence of alternative forms of a gene and giving lockers of a population
What do the levels of standing genetic variation predict
A species ability to adapt
What are some of the processes responsible for generating diversity
Mutation, sex, ploidy, balancing selection
What kind of mutations are passed on to the next generation
Germ line
What do germ line mutations include
Point mutations such as substitution, insertion, deletion and inversion
What mutations do not lead to changes
Synonymous and silent
What are some examples of Non-synonymous mutations
Missense, nonsense, frame change
Example of inversion mutations
Wading birds and their different male morphs: Independence, satellite and faeder
How do beneficial mutations arise?
Independent assortment, random fertilisation, crossing over, ploidy, balancing selection
What happens in independant assortment
Sexual reproduction mixes the DNA from the two haploid gametes to produce diploid offspring, when chromosomes line up, the chromosomes pull apart
What happens in crossing over
Flailing chromosomes exchange genetic material between the chromosome pairs
What happens in ploidy
Diploid means two copies of everything, the rarer the recesive allele, the greater the degree of protection from natural protection
What are the two types of balancing selection
Heterozygote advantage and frequency dependant selection
What happens in heterozygote advantage and example
The heterozygote s fittest over dominance for example sick cell anaemia in Africa is beneficial for patients with malaria so is maintained in the population
What happens in frequency dependant selection and the two type
The rare alleles have the highest fitness.
Postivie: fitness of a genotyoe goes up with its frequency- variation isnt maintained
Negative: fitness of genotype goes down as its frequnecy goes up- maintains frequency
Example of frequency dependant selection
Cichlid feed by taking mouthfuls of fish of the sides- Controlled by a single gene
Polymorphism definition
Differences between individuals of the same species
Divergence definition
Differences between individuals of different species
Molecular evolutionary terms
Evolution is changes in allele frequencies over time
a chromosome carries one possible allele at any given locus
mutation generates a new allele which can be inherited by its carriers descendants
Each new allele starts as a mutation in a single individual
Frequency of the allele can increase or decrease in each passing generation
What can the starting frequency if the new mutation be calculated with
1/(2N) - n is the population of diploid individuals
Who proposed the neutral theory and when
Mootoo Kimura in 1968
What does the neutral theory hypothesise
The the fate of most mutations contributing to molecular is determined by drift rather than selection
What are the assumptions in the neutral theory
The mutations are either neutral or weakly selected
How do we measure DNA sequence variation
Single nucleotide polymorphisms (SNPS)
What does the Wright-Fisher model do
It makes explicitly, testable predications about patterns of polymorphism and divergence
What are the assumptions of the Wright-fisher model
random mating, no selective differences, new individuals are formed by sampling at random with replacement of gametes produced by individuals
What is the Wright- fisher model equation
E(pi) = 4NeU
Whats the importance of the Wright-fisher model
Gives us a way of explaining patterns of genetic diversity
We can formally identify patterns of variation and use that to determine selective forces
Species with larger population size and higher mutation rates tend to be more variable
What are commonly used neutral markers
Synonymous polymorphisms, silent polymorphisms
What does Ne stand for
effective population size
What are the effects of populations bottlenecks on Ne
Loss of variability due to genetic drift being more rapid in smaller populations
Populations that experience bottlenecks are expected to have a low Ne
What do deleterious variants do
Tend to decrease in frequency in the population overtime
tend to segregate at lower frequencies than neutral variants
less likely to get fixed than neutral variants
could linger in the population for a substantial amount of time
What do beneficial variants do
Tend to increase in frequency in the population
Tend to segregate at higher frequencies than neutral alleles
More likely to get fixed than neutral variants
What do small Ne lead to
Much weakened selection, leading to deleterious mutations drifting to high frequencies
What is it predicted that repeated bottlenecks lead to
Deleterious variants being more common in non-African populations
What are the mutations in synonymous polymorphisms likely to be
Most mutations are probably neutral
What are mutations in non- synonymous polymorphisms likely to be
They’re likely to influence fitness
What is the rate of substitution equation under the rate of neutral molecular evolution
X= 2Nu x 1/(2N) = u
What does the rate of accumulation of new substitutions per generation depend on
The neutral mutation rate and independence of the population size
What is K
The expected number of substitutions per site between two homologous DNA sequences from two species
What is K proportional to
The mutation rate
What equation is used to estimate K
K = D/L
D- the total number of differences
L- the total number of sites considered
What does the neutral model predict in terms of time
Evolution should be constant over time since it depends only on the neutral mutation rate, u
What equation is used to predict mutation rate
T= K/ (2U)
What can patterns of point mutations be estimated using
Nucleotide substitutions
What are the feutures of the mammalian mitochondrial genome
Circular, double stranded DNA
15- 17 KB in length, 13 protein coding genes, 2 rRNA genes, 22 tRNA genes
A control region
What is the relative rate test equation
Kxa= Kxb
What is the generation time effect hypothesis
Errors in DNA replication in germ line cells is a major source of mutation
The hypothesis predicts a higher mutation rate per time unit in species with shorter generation time
How much of the human genome encodes for proteins
1%
How much of the human genome is conserved
5%
Characteristics of the tripartite motif protein
Primate genomes encode for defending themselves against retroviruses
What happened with the anti - malarial drug pyrimethamine
Introduced in 1970s, resistance spread to fixation in 6 years, it was induced by specific point mutations in active site of parasite
Why is population genetics needed?
Its not always clear what trait should be measured
We need to rule out chance effect
What does Tajimas D do
Compares the relative abundance of intermediate and low frequency variatiants
What does D< 0 mean
An excess of intermediate frequency variants
How to make a linkage mapping cross
- cross the two parental types
- Cross the hybrid offspring
- Recombination takes place during meiosis, shuffling the parental genomes around
- The progeny of F1 cross, inheriting recombined parental genomes
How to genotype a mapping cross
Place genome markers at regular places across the genome that distinguish two parental types
How to determine where the casusative gene is
Perform a statistical test at regular intervals along each chromosome to test for an association with the trait
Examples of an extended phenotype
Innates to the animal e.g. burrowing behaviour of mice
What are skyscrapers in manhatton plots
Regions with genes that explain variation
What is the fixation index
The inbreeding in subpopulations (S) is relative to in the total population (T)
What did Sewall Wright propose
Inbreeding could be used as a measure of differentiation among subpopulations
What is the fixation index equation
Fst = (Ht- Hs)/Ht
Hs: the average heterozygosity in the subpopulation
H1 is the expected heterozygosity in the total population
Whats the scale for FST
0-1
O means no differentiation
1 is a fixed differentiation
What can we use to predict the gene flow
Nm (number of migrants in each generation)
How can we sample differentiation of genes
Microsatellites, SNPS, Sequencing whole genomes
What is involved in microsatellites
Repeats of 2-5 base pairs in non coding areas, can be amplified using PCR
Disadvantages and advantages with sequencing whole genome
More costly, more resolution, can detect bigger mutations
Example 1: Arabidopsis lyrate on serpentine soils
25 individuals from 4 populations, detected 8.4 million polymorphisms across the genome, 96 had allele frequency differences of greater than 80% between soil types
Why do small horns/ scurns persist when they have costs to male reproductive success
Horns is determined by many genes of small effect and are just an indicator of quality
Genes associated with small horns confer a fitness advantage in females
Genes associated with samll horns have some other benifit to males
What are the two social forms of fire ants
Monogynes: single queen
Polygynes: multiple queens that are smaller
What are the two different forms of fire ants determined by
GP-9 gene
What is a super gene
A number of tightly linked genes that are not affected by recombination
What is cis-regulatory variation
Mutations/ regions that occur very close to the gene that the gene is regulating
What happens at the promoter of a gene
Where transcription is initiated, RNA will bind to that promoter to initiate transcription
What do enhancers do
Transcription factors bind and interact to the promoter and can be controlled by different enhancers
What happens post- transcriptionally
Alternative splicing, allows you to alter the sequence of the final protein, can remove exons after transcription or keep them to create different sequences of exons
